Table 3

Genes with functional annotation that are up-regulated in cBF as compared to PF-loga

Description

SysID (fold changeb, signal in cBF)


Nucleic acid

cold shock DNA binding domain protein

Tb927.4.4520 (3.8, 11127), Tb927.8.7820(3.1, 30733)

DNA binding motif protein

Tb927.8.8270 (2.1, 5130)

methylated DNA binding motif protein

Tb09.160.1490 (2.1, 6911)

SNF2 DNA repair protein

Tb927.7.4650 (3.6, 9704)

DNA topoisomerase II

Tb11.01.3390 (2.2, 20052)

heterogeneous nuclear ribonucleoprotein H/F

Tb927.2.3880 (2.5, 19993)

RNA-binding protein

Tb927.6.3480 (4.6, 15068), Tb927.7.3730 (2.4, 19060), Tb927.8.2780 (4.1, 22483, Tb10.389.1640 (2.9, 4885), Tb11.01.3940 (2.9, 6039)

Interaction Motifs

hypothetical conserved, ankyrin repeat

Tb11.01.6010 (2.1, 9639), Tb927.7.1420 (2.2, 13373)

hypothetical conserved, FHA and BRCT domains

Tb927.4.500 (2.6, 10222)

hypothetical conserved, PX domain

Tb927.7.4500 (2.3, 19542)

hypothetical conserved, RING finger

Tb10.70.3560 (2.4, 6310)

hypothetical conserved, zinc finger

Tb10.389.0740 (7.6, 16571), Tb10.70.2020 (4.7, 8391), Tb11.01.0220 (2.7, 20691), Tb10.70.1850 (2.7, 3725), Tb09.211.1720 (2.5, 18066), Tb927.3.5390 (2.3, 3358), Tb11.01.0090 (2.1, 19108), Tb11.02.2470 (2.0, 15163), Tb11.01.8270 (2.3,18420)

leucine-rich repeat protein

Tb11.02.1564 (5.1, 5086), Tb927.3.1490 (4.8, 3199), Tb927.3.580 (3.2, 7044), Tb11.02.1580 (2.2, 15932)

zinc-binding protein (Yippee)

Tb927.6.4810 (1.9, 3902)

Metabolism

acidic phosphatase

Tb927.5.610 (3.9, 21844)

acidocalcisomal pyrophosphatase VSP1

Tb11.02.4930 (2, 21100)

alternative oxidase

Tb10.6k15.3640 (5.2, 25749)

arginine kinase

Tb09.160.4570+1 (2.1, 8792)

aspartate aminotransferase

Tb10.70.3710 (2.2,10132)

ATP-dependent phosphofructokinase

Tb927.3.3270 (2.7, 35922)

Diacylglycerol kinase catalytic domain

Tb927.8.5140 (2.2,16973)

sphingolipid delta 4 desaturase

Tb927.6.3000 (2.3,10540)

fructose-1,6-bisphosphatase

Tb09.211.0540 (2.3,13478)

glutathionylspermidine synthetase

Tb11.12.0016 (2.1, 20983)

guanine deaminase

Tb05.5K5.200+1 (2, 7271)

haloacid dehalogenase-like hydrolase

Tb11.01.0120 (2.3, 8482)

hexokinase 1

Tb10.70.5820* (13.4, 27920)

hypothetical conserved, serine-esterase like motif

Tb11.01.3580 (2.2, 10321)

iron/ascorbate oxidoreductase family protein

Tb927.2.6180 (13.2, 6052), Tb927.2.6230 (6.9, 13271), Tb927.2.6310 (3.3, 8181)

lipase domain protein

Tb927.3.3870 (3.1, 13228)

nucleoside phosphorylase

Tb927.8.4430 (3.2, 23275)

phosphoglycerate kinase, glycosomal

Tb927.1.700* (10.1, 32849)

pyruvate kinase 1

Tb10.61.2680* (3.5, 35164)

sphingomyelin synthase family

Tb09.211.1020 (3.1, 9771), Tb09.211.1010 (2.3,)12554

Protein or lipid phosphorylation

casein kinase I, CK1

Tb10.70.5340 (2.6,12672)

cdc2-related protein kinase

Tb11.47.0031 (3.1, 15760)

cyclin 3, mitotic cyclin

Tb927.6.1460 (2.4, 11043)

dual specificity phosphatase

Tb11.02.1640 (2.3, 5100)

protein kinase

Tb927.5.3320 (2.4, 6629)

serine/threonine-protein kinase, NEK family

Tb927.2.2120 (2.2, 11101), Tb927.4.5310 (2.6, 13985), Tb927.8.7110 (2, 16132)

TFIIF-stimulated CTD phosphatase

Tb927.3.3380 (3, 8247), Tb10.61.2520 (2.5, 16649)

Protease-related

calpain cysteine peptidase

Tb927.8.8330 (3.3, 19000)

cysteine peptidase C

Tb927.6.560 (2, 17546)

Gp63 major surface protease homolog

Tb11.02.5310 (2.3, 16249), Tb10.70.5290* (5.2,14867), Tb11.02.5630 (4.2, 10649), Tb11.02.5610 (3.7, 6645), Tb11.02.5640 (3.3, 12431), Tb11.0370 (3.6, 4695), Tb11.0380 (2.6, 10329), Tb11.0360 (3.4, 9307)

hypothetical conserved, OTU protease domain

Tb927.8.5050 (2.2, 13601)

hypothetical conserved, UIM domain

Tb10.70.1130 (2.2, 20751)

inhibitor of cysteine peptidase chagasin family

Tb927.8.6450 (2, 29643)

metacaspase

Tb11.02.0730 (2.4, 11810), Tb927.6.930 (3, 1906), Tb10.70.5250 (15.1, 15483)

serine carboxypeptidase (CBP1)

Tb10.70.7090 (3.9, 16383)

serine peptidase

Tb927.3.4230 (2.7, 11496)

signal peptidase type I

Tb927.5.3220 (2.2, 13695)

Protein folding, modification and transport

acetyltransferase

Tb927.1.4490 (2.7, 4473)

ADP-ribosylation factor

Tb11.01.6060 (2.2, 4625)

chaperone protein DNAJ

Tb927.4.3980 (3.4, 10760), Tb927.6.3120 (2.5, 17514)

dynamin vacuolar sortin protein 1

Tb927.3.4720 (2.3, 13449)

GPI inositol deacylase precursor

Tb10.70.2420 (2.6, 21099)

heat shock protein HSP70-like protein

Tb09.160.3090 (2.4, 26203)

HSR1-related GTP binding protein

Tb927.4.2380 (2.0, 16054)

hypothetical conserved, TRAP alpha motif

Tb927.7.2190 (2.1, 3176)

oligosaccharyl transferase subunit

Tb927.5.890 (2.9, 10460)

protein disulfide isomerase, bloodstream-specific

Tb10.6k15.2290 (2.4, 28599)

UDP-Gal/GlcNAc-dependent glycosyltransferase

Tb927.3.5660 (2.0, 9638), Tb927.7.300 (2.1, 19406)

Surface or secreted, transporters

64 kDa invariant surface glycoprotein

Tb927.5.1390 (5.5, 7559), Tb927.5.1430 (3.6, 6582), Tb927.5.1410* (17.1, 5352), Tb927.2.3270* (6.9, 18103), Tb927.2.3300* +3 (5.6, 13407), Tb927.2.332* (8.1, 14544), Tb11.47.0001* (3.3, 10214)

75 kDa invariant surface glycoprotein

Tb927.5.350 (2.4, 13044), Tb927.5.360-Tb927.5.360b (4.7, 17510), Tb927.5.370 (6.2, 11233), Tb927.5.400 (4.2, 13688), Tb927.5.390* (5.9, 17712)

acidic phosphatase (ISG65-like)

Tb927.5.630 (3.7, 29580)

flagellum-adhesion glycoprotein

Tb927.8.4060 (4.5, 11088)

glycophosphatidylinositol phospholipase

Tb927.2.600* (3.4, 17679)

haptoglobin-hemoglobin receptor

Tb927.6.440 (4.0, 15595)

ABC transporter

Tb11.02.3950 (2.1, 11483)

adenosine transporter

Tb927.5.286b (2.3, 9396), Tb927.2.6200 (19.5, 2940), Tb927.2.6220 (20.7, 3409), Tb927.2.6320 (8.4, 10291), Tb927.2.6280 (20.1, 7137), Tb927.2.6240 (20.7, 7104)

amino acid transporter

Tb927.4.4020 (2.7, 26379), Tb927.4.4860 (2.3, 9610)

aquaglyceroporin

Tb10.61.2650 (4.2, 28913)

glucose transporter

Tb10.6k15.2040 (2.7, 48061), Tb10.6k15.2030 (4.4, 23370)

glycerol uptake protein

Tb10.61.0380 (2.3, 11746)

major facilitator superfamily protein

Tb927.3.4070 (5.3, 24190), Tb927.3.4090 (5.1, 9918), Tb10.61.2750 (2.5, 8885)

UDP-galactose transporter

Tb927.4.1640 (2.3, 5225)

Vacuolar-type Ca2+-ATPase 2

Tb927.8.1200 (2.5, 14542)

Other

kinesin

Tb10.61.1750 (5.0, 24612), Tb927.6.4390 (2.4, 12826), Tb927.7.4110 (2.5, 4714)

nucleolar protein

Tb09.160.1180 (2.3, 4877)

procyclin-associated gene

Tb10.70.1310 (3.6, 9070), Tb10.70.1300 (9.9, 7362), Tb11.01.6210 (3.3, 22849), Tb11.01.6220 (4.1, 10444)

retrotransposon hot spot protein

Tb09.v4.0013 (7.2, 3458), Tb09.244.2180 (2.8, 1283)

sarcoplasmic reticulum glycoprotein

Tb10.61.1710 (2.0, 9921)

VSG-related

Tb927.1.5060 (2.5, 5925), Tb927.1.5170 (7.0, 8241), Tb927.2.2060 (3.1, 8575), Tb927.3.1470-Tb927.3.1520 (4.3, 7116), Tb927.3.1500 (33.1, 13722), Tb927.3.1510 (12.5, 1450) Tb927.3.2540 (3.3, 2297), Tb927.3.5680 (6.1, 1903), Tb927.5.110 (4.1, 1468), Tb927.5.130 (5.4, 5216), Tb927.8.7300+1 (3.7, 16812), Tb09.160.5350 (3.4, 9129), Tb09.v1.0300+1 (4.4, 6354), Tb09.v1.0290+1 (4.2, 6386), Tb09.244.2330 (5.2, 3974), Tb09.244.2310 (7.6, 2584), Tb09.244.2280 (3.1, 881), Tb09.244.2240 (5.1, 2605), Tb09.244.2200 (4.3, 2404), Tb11.02.1566 (8.0, 12758)


aESAGs, GRESAGS, VSGs are not included. A complete list of the genes is found in Additional file 3.

bBold: gene was upregulated in all BF vs all PF conditions. Probe-sets detecting >1 gene indicated by "+", plus number of additional genes.

* marks known stage-regulated genes used in previous array study [12].

Jensen et al. BMC Genomics 2009 10:482   doi:10.1186/1471-2164-10-482

Open Data